backgroundCorrect.SNP {beadarraySNP} | R Documentation

## Background correction

### Description

Perform background correction on Illumina Golden Gate bead arrays

### Usage

       backgroundCorrect.SNP(object,method=c("none", "subtract", "half", "minimum",
                             "edwards", "normexp", "rma"),offset = 0)

### Arguments

`object` | SnpSetIllumina object
`method` | character, method of correction
`offset` | numeric, constant to add after correction

### Details

Code has been ported from the `limma` package. The matrices `Gb` and `Rb` should be available in the `arrayData` slot of the object.

### Value

This function returns an `SnpSetIllumina` object with background corrected values in the `G` and `R`.

### Author(s)

Jan Oosting, based on `limma` package by G. Smyth

### See Also

`SnpSetIllumina-class`, `backgroundCorrect`,

`backgroundEstimate`, `normalizeBetweenAlleles.SNP`, `normalizeWithinArrays.SNP`

### Examples

      ## Not run: data.bg<-backgroundCorrect.SNP(data.raw,"subtract")

[Package beadarraySNP version 1.60.0 Index]